Phosphogypsum, an industrial byproduct of fertilizer manufacturing, has marginal economic value leading to its accumulation in phosphogypsum stacks. When not properly maintained, these facilities can become a source of nutrients and threaten coastal water quality. Nutrient-rich industrial wastewater from the Piney Point phosphogypsum facility has been discharged into the Tampa Bay estuary several times since the 1960s. These discharge events prompt concern about their effect on water quality, nutrient cycling, aquatic biota, and ecosystem services. This study investigated how historic discharge events from Piney Point contributed to sediment, nutrient, and radionuclide accumulation using bulk nutrient concentrations and stable- and radioisotopes. Additionally, pigment biomarkers were used to assess if these events are linked to regime shifts in phytoplankton assemblages. At both sites photosynthetic pigment concentrations were highest in the top sediment intervals with the greatest increase in pigments associated with diatoms, green algae, and cyanobacteria. At Bishop Harbor, the mean ²²⁶Ra activity (3.9 + 0.8 dpm g^-1) was ~10-fold greater than at Piney Point Creek (0.4 + 0.3 dpm g^-1). Likewise, the excess ²¹⁰Pb inventory (82.4 + 13.5 dpm cm^-2) at Bishop Harbor was ~3-fold greater than at Piney Point Creek (27.0 + 1.7 dpm cm^-2). Total phosphorus concentrations and accumulation rates at Bishop Harbor ranged from 8.7 to 14.4 mg g^-1 and 141 to 293 g m^-2 y^-1, respectively, suggesting that an excessive amount of phosphorus from these discharge events was deposited in the sediments. This legacy phosphorus may be susceptible to remobilization by diffusive flux and resuspension events, such as storms, which may further contribute to coastal eutrophication.